We present **JPharmatron**, a Japanese domain-specific large language model (LLM) for the pharmaceutical field, developed through continual pre-training on two billion Japanese pharmaceutical tokens and eight billion English biomedical tokens. For rigorous evaluation, we introduce **JPharmaBench**, a benchmark suite consisting of three new benchmarks: YakugakuQA, based on national pharmacist licensing exams; NayoseQA, which tests cross-lingual synonym and terminology normalization; and SogoCheck, a novel task involving cross-document consistency checking.We evaluate our model against open-source medical LLMs and commercial models, including GPT-4o. Experimental results show that **JPharmatron** outperforms existing open models and achieves competitive performance with commercial ones.Interestingly, even GPT-4o performs poorly on SogoCheck, suggesting that cross-sentence consistency reasoning remains an open challenge.**JPharmatron** enables secure and local model deployment for pharmaceutical tasks, where privacy and legal constraints limit the use of closed models. Besides, **JPharmaBench** offers a reproducible framework for evaluating Japanese pharmaceutical natural language processing. Together, they demonstrate the feasibility of practical and cost-efficient language models for Japanese healthcare and pharmaceutical sectors.Our model, codes, and datasets are available on HuggingFace: https://huggingface.co/collections/EQUES/jpharmatron and https://huggingface.co/collections/EQUES/jpharmabench.

This paper investigates the effect of tokenizers on the downstream performance of pretrained language models (PLMs) in scriptio continua languages where no explicit spaces exist between words, using Japanese as a case study. The tokenizer for such languages often consists of a morphological analyzer and a subword tokenizer, requiring us to conduct a comprehensive study of all possible pairs. However, previous studies lack this comprehensiveness. We therefore train extensive sets of tokenizers, build a PLM using each, and measure the downstream performance on a wide range of tasks. Our results demonstrate that each downstream task has a different optimal morphological analyzer, and that it is better to use Byte-Pair-Encoding or Unigram rather than WordPiece as a subword tokenizer, regardless of the type of task.